Contacts of the helix formed by residues 140 - 151 (chain B) in PDB entry 2QVS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 140 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ASN 4.0 1.6 + - - -
139B LEU* 1.3 78.1 - - - +
141B GLN* 1.3 65.0 + - - +
142B GLU* 3.2 10.1 + - - +
143B GLN* 2.5 60.6 + - - +
144B LEU* 3.2 18.1 + - - +
240B ASN* 3.9 1.1 - - - +
244B LYS* 2.8 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLN* 5.8 5.7 + - - +
140B ASP* 1.3 74.9 - - - +
142B GLU* 1.3 64.6 + - - +
144B LEU* 3.4 8.1 + - - +
145B SER* 3.2 22.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ASP* 3.2 8.2 + - - +
141B GLN* 1.3 77.4 - - - +
143B GLN* 1.3 67.6 + - - +
145B SER* 3.0 14.0 + - - -
146B GLN* 2.9 56.9 + - - +
240B ASN* 4.1 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 4.0 16.4 - - + +
140B ASP* 2.5 60.4 + - - +
142B GLU* 1.3 71.8 - - - +
144B LEU* 1.3 57.2 + - - +
146B GLN* 3.3 10.5 + - - +
147B VAL* 2.8 35.6 + - - +
236B ILE* 5.0 1.8 - - + -
237B ILE* 3.6 36.5 - - + +
240B ASN* 3.3 24.8 - - + +
241B ASN* 3.2 25.9 + - - +
244B LYS* 4.1 2.0 - - - +
213E LYS* 5.4 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLN* 3.4 38.1 - - + +
130B CYS* 5.2 5.4 - - + -
136B PHE* 4.2 32.3 - - + +
139B LEU* 4.7 18.0 - - + +
140B ASP 3.2 15.9 + - - +
141B GLN* 3.6 7.6 - - - +
143B GLN* 1.3 77.8 - - - +
145B SER* 1.3 57.3 + - - +
147B VAL* 3.4 3.8 + - + +
148B LEU* 2.9 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ARG* 3.0 19.4 + - - +
141B GLN* 3.2 11.1 + - - -
142B GLU* 3.0 19.0 + - - -
144B LEU* 1.3 76.4 - - - +
146B GLN* 1.3 61.2 + - - +
148B LEU* 3.2 1.4 + - - -
149B ASP* 2.9 41.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B VAL* 5.7 1.0 - - - +
142B GLU* 2.9 45.3 + - - +
143B GLN* 3.7 5.2 - - - +
145B SER* 1.3 76.1 + - - +
147B VAL* 1.3 62.1 + - - +
149B ASP* 3.3 13.8 - - - +
150B ALA* 3.1 17.0 + - - +
236B ILE* 3.4 40.1 + - + +
240B ASN* 3.9 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 3.8 31.0 - - + -
139B LEU* 4.9 3.6 - - + -
143B GLN 2.8 20.5 + - - +
144B LEU* 3.6 8.3 - - + +
146B GLN* 1.3 74.3 - - - +
148B LEU* 1.3 70.0 + - + +
150B ALA* 3.1 13.3 + - - +
151B MET* 3.3 13.6 + - + +
228B LEU* 4.0 17.6 - - + +
233B PHE* 4.0 15.0 - - + -
236B ILE* 3.9 25.1 - - + -
237B ILE* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LYS* 2.9 30.4 + - - -
123B ARG* 3.3 43.3 - - - +
126B LEU* 4.1 17.0 - - + -
127B GLN* 3.7 30.1 - - + -
130B CYS* 4.8 10.3 - - - -
136B PHE* 5.3 0.2 - - + -
144B LEU* 2.9 33.5 + - + +
145B SER* 5.4 0.4 - - - -
147B VAL* 1.3 76.8 - - + +
149B ASP* 1.3 65.9 + - - +
151B MET* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B VAL* 4.4 12.8 - - + +
116B HIS* 3.9 28.9 + - - +
118B LYS* 3.9 3.5 + - - +
123B ARG* 2.4 39.0 + - - +
145B SER* 2.9 26.9 + - - +
146B GLN* 3.3 16.0 - - - +
148B LEU* 1.3 79.2 - - - +
150B ALA* 1.3 60.4 + - - +
151B MET 3.2 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B VAL* 4.2 20.2 - - + +
116B HIS* 3.5 10.4 + - - -
146B GLN 3.1 1.0 + - - +
147B VAL 3.1 10.4 + - - +
149B ASP* 1.3 78.6 - - - +
151B MET* 1.3 62.3 + - - +
152B PHE* 3.2 9.5 + - - -
227B GLY 4.4 0.2 - - - +
228B LEU* 4.5 8.6 - - + +
232B THR* 3.7 21.0 - - + +
236B ILE* 3.6 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B HIS* 3.4 7.1 - - - +
118B LYS* 2.6 30.9 + - - +
126B LEU* 4.1 14.4 - - + -
130B CYS* 5.3 1.3 - - - -
136B PHE* 5.2 3.8 - - + -
147B VAL* 3.4 18.4 - - - +
148B LEU* 3.0 33.8 + - - +
150B ALA* 1.3 75.1 - - - +
152B PHE* 1.3 61.8 + - - +
172B PHE* 4.1 21.1 - - + -
174B VAL* 4.2 10.5 - - + -
226B TRP* 3.6 29.6 - - + +
227B GLY 3.3 11.7 - - - +
228B LEU* 3.7 32.1 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il